Abstract 1478: Broad downregulation of normal-specific super-enhancer associated genes in lung adenocarcinoma
Authors: Guoshuai Cai, Yihan Liu, Xiang Cui, Christopher Amos, Feifei Xiao
Journal: Cancer Research (2023)

Abstract Background Lung adenocarcinoma (LUAD) is the most common histologic subtype of lung cancer and a highly heterogeneous disease whose mechanism is not fully uncovered. Recently, Super-enhancers (SEs), tissue-specific clusters of enhancer elements, were found to drive cell identity genes and play an important role in tumorigenesis. However, current studies focus on SE in lung tumors but largely neglect those specific in normal lung tissues, which also provide critical data for understanding transformation of normal cells into cancer cells. For the first time, this study characterized normal-specific SE-associated genes (SEGs) in LUAD by dysregulation in tumor, prognostic significance and tumor microenvironment (TME) interactions via a comprehensive analysis of 22 bulk and single-cell transcriptomic datasets. Methods We analyzed TCGA datasets of 10 cancer types, and additional datasets comprising 4 datasets of LUAD tumor and normal paired samples, 5 datasets of LUAD tumors with survival information, and 3 single-cell transcriptomic datasets. For each dataset, standard methods were used for data preprocessing and normalization according to its generation platforms (e.g., microarray, bulk RNA-seq and scRNA-seq). For downstream analyses, paired t-test and linear model were used to identify dysregulated SEGs; Cox Proportional Hazards Regression was used to evaluate their prognostic significance and LASSO was used to select features for building multivariate prognostic models; bulk data deconvolution and correlation analysis were applied to assess the association of TME cell composition and SEG expression; Gene set enrichment analysis was applied for functional analysis. Results We found normal-lung SEGs were significantly disproportionally downregulated in LUAD tumors (Chi-squared test, p &amp;lt; 0.01), and associated with poor prognosis of patients. The patterns were consistently found in discovery (TCGA) and independent validation datasets. Interestingly, the effect appears specific to lung as such downregulation of normal-lung SEGs was also found in lung squamous cell carcinoma but not observed in most of other 8 cancer types. The downregulated SEGs were significantly involved in cell differentiation, apoptosis, proliferation, and stem cell pluripotency, and were enriched in tumor suppressors. Also, their downregulation correlate with reduced endothelial cells and lower immune activity with reduced B and CD8 T cells and inhibited immune target genes. Conclusions Our study characterized the genes associated to normal-specific SEs in LUAD, shedding sheds light on their role in tumorigenesis of lung cancers. Their broad downregulation indicates a significant effect of SE aberrancy in the transformation of normal cell into cancer cells with a modulation of immune microenvironment; further functional studies are needed to elucidate the underlying mechanism. Citation Format: Guoshuai Cai, Yihan Liu, Xiang Cui, Christopher Amos, Feifei Xiao. Broad downregulation of normal-specific super-enhancer associated genes in lung adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1478.